wusage does a pretty good job, urgin is also a good stats package.
regarding php, here's a few pointers.
combine sql queries into big queries instead of lots of seperate small queries,
use table indexes, check with the mysql client to see the performance of your
queries, avoid slow queries, in my.cnf the mysql config file reduce the timeout
settings so connections get closed within a few seconds, if you have lots of
queries use mysql_pconnect (persistent connection). cache queries especially
if the results are always the same. check the html output, make sure it's
compliant, closing tags properly reduces rendering
compile your php pages with Zend SafeGuard, only use apache modules that
you really use, remove all the other modules
